275ch CTF stimulus channel and new CTF data format

Fri May 27 09:48:29 CEST 2005

Hi Sanja,

I had the same problem and I just created this kind of m-file:

function [d] = dist(A);
d = sum((A).^2).^0.5;

At least it works, I hope I didn't something wrong,

Best,

Stephan

At 03:13 26.05.2005 +0200, you wrote:
>Hi Robert,
>
>Your answer helped a lot but there was also another problem. My stimulus
>channel “on” states were not 9, but 5 or 6  samples long. That's why I was
>getting all zeros for both frontpanel and backpanel. I adjusted trigshift
>(line 60) to 0  as the trigger values were either 0 or the predetermined on
>values. For all of my datasets I've looked at so far, there is no rising
>time for the stimulus channel. So, I guess this is another (nice) change in
>the new CTF 275  acquisition program...
>
>On another note, I ran some timefrequency analyses on the sensor level and I
>wanted to plot the data using multiplotTFR. I'd like to use the information
>from the header when plotting the sensors.  However, if I use the
>gradiometer structure created with read_ctf_res4, i.e.  cfg.layout =
>hdr.grad, I get an error message
>??? Undefined command/function 'dist'.
>Error in ==> createlayout at 93
>    d = dist(prj');
>
>You mentioned in one of your previous replies that sensor position and
>information is not being read correctly for the new CTF 275 datasets. (BTW,
>what tells you that read_fcdc_header does not read it correctly?) If I use
>ctf_read_res4 (ctf2matlab toolbox as mentioned by Tom Holroyd) I should be
>getting correct gradiometer information (right?).Well. I tried it both ways
>and I get identical position information with read_ctf_res4 (fcdc) and
>ctf_read_res4 (nimh). Orientation information differs in that that nimh code
>stores only first coil orientation, whereas the fcdc code stores both coil
>orientations. Both codes adjust for the possibility that sometimes coil
>orientations stored in res4 file may be pointing toward center.
>
> It is still not clear to me what happens later with orientation information
>and what effect of using only first coil orientation would be... What I
>would ultimately like to do is to run time frequency analysis (on the sensor
>level first, but also on the virtual sensor level) for each subject in the
>group and be able to compare the results using some statistical approach.
>However, first I need to establish whether the data is correctly read.
>
>I appreciate your and any other fieldtriper help,
>
>Sanja
>
>
>On Fri, 6 May 2005 09:21:48 +0200, Robert Oostenveld
><r.oostenveld at FCDONDERS.RU.NL> wrote:
>
>>Hi Sanja,
>>
>><--let's move our email exchange over towards the discussion list-->
>>
>>On 5 May 2005, at 22:50, Sanja Kovacevic wrote:
>>
>>> Thank you for helping me with this. I changed the filetype and
>>> read_ctf_res.m files as you suggested, and I was able to read in the
>>> data, however now I got problem with definetrial.m. Actually, I think
>>> the problem is with read_ctf_trigger as the 275 CTF dataset does not
>>> have a channel named 'STIM' but 'UPPT001' (line 63 in
>>> read_ctf_trigger). That was easy to fix by replacing STIM with
>>> UPPT001.
>>>
>>> However, I don't understand why you use (line 70 and 71 in
>>> read_ctf_trigger.m)
>>>
>>> bpstim = fix(stim / 2^16);
>>> fpstim = double(bitand(uint32(stim), 2^16-1));
>>
>>WHen I started at the donders and implemented this, I was told that our
>>151 ch system has a "frontpanel" and a "backpanel". I never looked very
>>acurately at the electronics cabinet and all the cables that go into
>>it, but I guess that they refer to the way in which the cabinet is
>>placed in our lab. Somehow, the CTF system's own triggers are put on
>>the frontpanel, and the triggers that are generated on the stimulus PC
>>are put on the backpanel. Since people write their stimulus programs on
>>the presentations pc, and define/write trigger values in the 16
>>bit-range on that computer. They appear in the higher 16 bits of the 32
>>bit STIM channel, which is confusing since then the values don't match
>>the ones on the presentation computer. Therefore the 16 lowest and 16
>>highest bits are separated and treated separately. On line 70, the
>>highest 16 bits are shifted downward by 16 bits (i.e. divide by 2^16).
>>On line 71, the highest 16 bits are masked away, keeping only the
>>lowest 16 bits.
>>
>>> The trigger values on our CTF system use lower 8 bits, i.e. possible
>>> values of the triggers are from 0 to 255. I am now quite confused with
>>> what happens to my trigger values. The bottom line is that I have all
>>> zeroes for backpanel and frontpanel.
>>
>>I think that you should look at the so called "frontpanel" triggers
>>(whose bits are not shifted).
>>
>>> BTW, could you give me or point to an example of a user specified
>>> trialfun that would include trials where trigger with value of 10 ir
>>> trigger with value of 138 occurs?
>>
>>You mean either a 10 or a 138? Just from my head:
>>
>>function [trl] = trigger138(cfg)
>>hdr      = read_fcdc_header(cfg.dataset);
>>event    = read_fcdc_event(cfg.dataset);
>>trl      = [];
>>prestim  = 0.1;
>>poststim = 0.5;
>>for i=1:length(event)
>>   if strcmp(event(i).type, 'frontpannel trigger')
>>     if (event(i).value==10) | (event(i).value==138)
>>        % found trigger of interest
>>        trl(end+1,1) = event(i).sample - prestim*hds.Fs;
>>        trl(end  ,2) = event(i).sample + poststim*hds.Fs;
>>        trl(end  ,3) =                 - prestim*hds.Fs;
>>     end
>>   end
>>end
>>
>>You could put prestim and poststim (time in seconds) in the cfg
>>structure, to keep the function more flexible. From this example, you
>>caneasily  to make a conditional function, i.e. find the sample at
>>which a trigger 138 occurred and which was preceded by a trigger 10.
>>
>>Alternatively, you can also use the standard code, i.e. without a
>>custom trialfunction, to achieve the same. Try this:
>>
>>cfg = [];
>>cfg.dataset = 'something.ds';
>>cfg.trialdef.eventtype  = 'frontpannel trigger';
>>cfg.trialdef.eventvalue = [10 138];
>>cfg.trialdef.prestim    = 0.1;
>>cfg.trialdef.poststim   = 0.5;
>>cfg = definetrial(cfg);
>>
>>best regards,
>>Robert
>

-----------------------------
Dipl. Psych. Stephan Moratti
Dept. of Psychology
University of Konstanz
P.O Box D25
Phone: +40 (0)7531 882385
Fax: +49 (0)7531 884601
D-78457 Konstanz, Germany
e-mail: Stephan.Moratti at uni-konstanz.de

http://www.clinical-psychology.uni-konstanz.de/